I just finished the task of getting Incubation to run on Win10 (and that was complicated enough) and now I ran into the next problem right away:
Whenever I start the game, it always runs the Wilderness Missions campaign.
How do I get the base games campaign (the one with the intro, cutscenes and an actual story) to run?

Just create proper shortcuts manually.

Launcher.exe without parameters starts the original campaign.
Launcher.exe -addon starts the Wilderness Missions.

Good idea and thanks for the reply.
But checking the shortcuts was the very first thing I tried.
The Incubation shortcut reads Launcher.exe and the Incubation - The Wildewrness Missions reads Launcher.exe -addon
And still the game refuses to start the original campaign.
No matter what Shortcut I use, I always get the Add On started.
I also tried the Incubation.exe from the games installation folder, but it always results in 2 error messages:
Missing file: Autorun.dat, followed by: Global Exception -1
So might you have any other ideas? Since I'm pretty clueless now...

I got answer from the support and even though they couldn't help me, they where able to reproduce the issue.
So it's not just me! I hope that the community might find a solution at some point.
I'll stay tuned. And hopefull...

I solved the issue! I got Incubation running now!
But it required some further work though.
Since no one was able to help me, I attempted a last try to fix it myself.
I uninstalled it once more und installed it again, this time to the default folder (D:\Battle Isle Incubation).
Initially I had the game installed to "D:\Incubation", seemingly that was somehow the reason for that issue.
Now that I had installed it to "D:\Battle Isle Incubation", the game refused to run at all. I started the game, but nothing happend. *sigh*
So I dug into the forum once more and found out, that the game might run in 3Dfx mode.
Furthermore I learned, that the "Settings" file must be run as admin. All the other .exe files in this game do that by default... all of them but this one... *siiigh*
Now the unbelievable happend... the game started! Finally!! It runs!!!
But my enthusiasm was immediately curbed, when I saw the iconic intro sequence, all without speech. *siiiiigh*
So I did another search in the forum and learned, that the "Windows 98/Me kompatibility mode" might solve that issue...
And it did! Incubation runs now, with sound and speech in the cutscenes!

So thanks for the... uhm... I mean, thanks to... ugh... myself? ... uh... kind of? pew... however.

I hope this will be helpful to anyone who might run into the same issues.

Thanks!! Much appreciated!

It indeed is and I chose to dig even deeper. I am trying to run this on a Linux machine via wine. And it works, except for the same problem that you have and it only started the addon, not the base game. It's weird to say the least.

The base game starts when I install the game to one of those directories:
- C:\GOG Games\Battle Isle Incubation
- C:\Battle Isle Incubation
- C:\GOG Games\Incubation
- C:\abc

The base game does not start when I install it here:
- C:\Incubation

So it seems, that it's actually the C:\Incubation that's hardcoded somewhere to force the addon. Very weird. My first guess was that it's in the registry somewhere. But up to now, I was not successful at all at finding the right location.

I have one hint that it's not in the registry. If I copy all the created registry settings in the installation process to a new wine prefix, it again only starts the addon and not the base game. But what other files would the installer change? What is going on here?

I tried all those thing with the original installer (english version) and a changed installer (german version). All those locations do work with the modified, german version as well. So the file that is changed during installation seems to not be inside the game directory. But where could it be?